New Zealand researchers lead world-first sequencing of bilberry genome

A bilberry gene mapping project at Plant & Food Research, funded by Genomics Aotearoa, has made some significant findings on the berry’s unique pigments, something that has exciting potential for our own horticulture industry.

The genome produced by the project is a world first, but, not only that, the researchers were also excited to find a genetic marker for the distinctive colour of the fruit.

The bilberry is a shrub found across much of northern European and as far north as the Arctic Circle. It grows wild, and its dark-coloured berries are harvested for food and medicinal purposes.

It belongs to the same genus – Vaccinium – as North American blueberries but unlike the pulp of blueberry, which is light green, the bilberry is distinctly red or purple. Continue reading

Disease-resistance – the hardy wild grass that could save our bread

An obscure species of wild grass contains “blockbuster” disease resistance that can be cross-bred into wheat to give immunity against one of the deadliest crop pathogens.

A collaborative international team of researchers identified the stem rust resistance gene from the wild goat grass species Aegilops sharonensis.

The research team led by the John Innes Centre, The Sainsbury Laboratory, and the University of Minnesota used bioinformatic advances to develop the first accurate genome map of Aegilops sharonensis.

The genetic potential of this hardy relative of wheat found in Israel and southern Lebanon has been largely unexplored.

Using the genetic map and a search tool technique called Mutant Hunter, the team scanned the genome for mutations looking for ones which were different in plants that were immune to stem rust, a disease which has troubled farmers for millennia.

This search identified a candidate gene, which the researchers thought was responsible for protecting plants. Using molecular tweezers, they isolated the gene of interest and transferred it into a susceptible plant, where it conferred strong protection against all tested strains of the wheat stem rust fungus, Puccinia graminis f. sp. tritici.

Dr Brande Wulff, a wheat researcher at King Abdullah University of Science and Technology (KAUST), formerly a group leader at the John Innes Centre and one of the authors of the study, said:

“We now have this blockbuster gene that confers amazing immunity. If I were stem rust, I would be shaking in my spore.”

It had been an arduous research journey lasting many years, said John Innes Centre researcher Dr Guotai Yu, first author of the study.

“… but we have now found this gene that confers broad-spectrum resistance. We have yet to come across an isolate of the pathogen which can overcome the gene.” 

In this study which appears in Nature Communications, experiments showed that the Sr62 gene encodes a molecule called a tandem protein kinase. Ongoing studies are looking at how this gene functions so researchers can biologically engineer the mechanism to be more efficient.

The research team plans to employ the new gene as part of a stack of genes — bred into commonly used wheat varieties — using genetic modification technology.

They predict more resistance genes will be identified in and cloned from populations of Aegilops sharonensis and other wild grasses using their methods of gene discovery and deployment.

Aegilops sharonensis is known to possess many traits of agricultural importance such as resistance to major diseases including rusts.

However, its long generation time, tough seed coat, and difficulties of crossing it with wheat cultivars have made it less tractable than other species of wild grasses being mined for useful genetic traits.

This makes the findings in this study even more valuable, explains Professor Brian Steffenson from the University of Minnesota and co-author of the study:

“Given the great difficulties in crossing Aegilops sharonensis to wheat, we were fairly certain that the rust resistance genes discovered in the wild species would be novel.” 

Aegilops sharonensis has a very narrow habitat range along the coastal plain of the Mediterranean Sea.

Professor Steffenson adds:

“It is therefore timely and important that efforts were made to collect and characterize accessions of this species before they are lost to urbanization. It is our hope that the resistance gene cloned in this research will, when combined other genes, confer long-lasting resistance in wheat varieties, thereby reducing the threat of the stem rust disease”

The study highlights recent developments in Latin America where GM (Genetically Modified) wheat engineered for drought tolerance has been approved — potentially paving the way for GM traits to be bred into wheat more widely in the face of the climate crisis.

The search for resistance against stem rust has become more urgent as epidemics of the disease are becoming more frequent and climate change threatens to further increase its spread.

“Pathogens like stem rust, already reduce the yield of wheat by 21 per cent. Not only is the grain itself lost or damaged by the pathogen, but also the energy that goes into production — an equivalent of 420 billion kilowatts — enough to power 300 million homes in the developing world is wasted. If we can intervene with genetics, by recruiting the resistance found in this wild-wispy looking grass then that would be an amazing contribution to agriculture and climate change,” said Dr Wulff.

Journal Reference:

  1. Guotai Yu, Oadi Matny, Nicolas Champouret, Burkhard Steuernagel, Matthew J. Moscou, Inmaculada Hernández-Pinzón, Phon Green, Sadiye Hayta, Mark Smedley, Wendy Harwood, Ngonidzashe Kangara, Yajuan Yue, Catherine Gardener, Mark J. Banfield, Pablo D. Olivera, Cole Welchin, Jamie Simmons, Eitan Millet, Anna Minz-Dub, Moshe Ronen, Raz Avni, Amir Sharon, Mehran Patpour, Annemarie F. Justesen, Murukarthick Jayakodi, Axel Himmelbach, Nils Stein, Shuangye Wu, Jesse Poland, Jennifer Ens, Curtis Pozniak, Miroslava Karafiátová, István Molnár, Jaroslav Doležel, Eric R. Ward, T. Lynne Reuber, Jonathan D. G. Jones, Martin Mascher, Brian J. Steffenson, Brande B. H. Wulff. Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62Nature Communications, 2022; 13 (1) DOI: 10.1038/s41467-022-29132-8

Source:  ScienceDaily

Meat Board announces investment in innovative beef genetics programme

The New Zealand Meat Board (NZMB) is to invest up to $1 million a year in the ground-breaking Informing New Zealand Beef (INZB) genetics programme.

The decision, which is subject to consultation with farmers, will see the NZMB joining the Ministry for Primary Industries (MPI) and Beef + Lamb New Zealand (B+LNZ) in supporting the seven-year Sustainable Food & Fibre Futures (SFF Futures) partnership, which aims to boost the sector’s profits by $460m over the next 25 years.

The INZB programme is focused on increasing the uptake of the use of genetics in the beef industry. The five main components of the programme are building a genetic evaluation and data infrastructure, progeny test herds, developing breeding objectives and indexes, developing new data sources and supporting farmer uptake of new genetic information. Continue reading

Sequencing of genetic material facilitates the breeding of new potato varieties

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Scientists have deciphered the highly complex genome of the potato, a technical feat that will accelerate efforts to breed superior varieties.

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Scientists at the Ludwig-Maximilians-Universität München and the Max Planck Institute for Plant Breeding Research in Cologne have decoded the highly complex genome of the potato. This technically demanding study – more than 20 years after the first release of the human genome – lays the biotechnological foundation to accelerate the breeding of more robust varieties, an important step for global food security.

When shopping for potatoes today, buyers may well be going home with a variety that was available more than 100 years ago. Traditional potato varieties are popular.

This highlights a lack of diversity among the predominant potato varieties.

But researchers in the group of geneticist Korbinian Schneeberger, by generating the first full assembly of a potato genome, have paved the way for breeding new varieties:

“The potato is becoming more and more integral to diets worldwide including even Asian countries like China where rice is the traditional staple food. Building on this work, we can now implement genome-assisted breeding of new potato varieties that will be more productive and also resistant to climate change — this could have a huge impact on delivering food security in the decades to come.”

The low diversity makes potato plants especially susceptible to diseases. This can have stark consequences, most dramatically during the Irish famine of the 1840s, where for several years nearly the entire potato crop rotted in the ground and millions of people in Europe suffered from starvation simply because the single variety that was grown was not resistant to newly emerging tuber blight.

During the Green Revolution of the 1950s and 1960s, scientists and plant breeders succeeded in achieving large increases in the yields of many of our major crop staples like rice or wheat. However, the potato has seen no comparable boost, and efforts to breed new varieties with higher yields have remained largely unsuccessful.

The reason for this is simple but has proven difficult to tackle — instead of inheriting one copy of every chromosome from both the father and from the mother (as in humans) potatoes inherit two copies of each chromosome from each parent.

This makes them a species with four copies of each chromosome (tetraploid). Four copies of each chromosome also mean four copies of each gene, which makes it highly challenging and time-consuming to generate new varieties that harbour a desired combination of individual properties.

Furthermore, multiple copies of each chromosome make the reconstruction of the potato genome a far greater technical challenge than was the case for the human genome.

The researchers have overcome this long-standing hurdle using a simple yet elegant trick. Instead of trying to differentiate the four, often very similar, chromosome copies from each other, Korbinian Schneeberger, his colleague, Hequan Sun, and other co-workers circumvented this problem by sequencing the DNA of large numbers of individual pollen cells.

In contrast to all other cells, each pollen cell contains only two random copies of each chromosome; this facilitated the reconstruction of the sequence of the entire genome.

An overview of the complete DNA sequence of cultivated potato has the potential of greatly facilitating breeding and has been an ambition of scientists and plant breeders alike for many years already. With this information in hand, scientists can now more easily identify gene variants responsible for desirable or undesirable.

Journal Reference:

  1. Hequan Sun, Wen-Biao Jiao, Kristin Krause, José A. Campoy, Manish Goel, Kat Folz-Donahue, Christian Kukat, Bruno Huettel, Korbinian Schneeberger. Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivarNature Genetics, 2022; DOI:

Source:  ScienceDaily

Plant & Food Research and Lincoln University part of game-changing gene discovery

Scientists from Plant & Food Research and Lincoln University have contributed knowledge integral to the discovery of a new gene described as a game-changer for global agriculture.

The gene allows natural reproduction by cloning in plants, allowing highly desirable traits to be carried through to the next generation rather than lost when the plants reproduce through pollination.

The New Zealand scientists have been working with scientists in the Netherlands (at research company KeyGene and Wageningen University & Research or WUR) and Japan (at breeding company Takii) to identify ways to produce plant seeds that are genetically identical to the parent plant.

The research was recently published in the prestigious journal Nature Genetics.

The newly discovered gene, named PAR, controls parthenogenesis, a process whereby plant egg cells spontaneously grow into embryos without fertilisation. Normally, the PAR gene is triggered by fertilisation, but in plants that reproduce by apomixis – a type of reproduction which does not require fertilisation – the PAR gene switches on spontaneously, so the egg cells are triggered to start dividing into a new embryo. Continue reading

Gene therapy developed by Lincoln scientists receives US FDA approval for in-human clinical trial

A Lincoln research team has received US FDA approval for in-human clinical trials of their gene therapy for the treatment of CLN5 Batten disease, a fatal neurodegenerative childhood disease.

The CLN5 form of Batten disease appears early in a child’s life and causes brain degeneration manifesting in devastating symptoms including vision loss, seizures, dementia, abnormal movements and inability to communicate. Sufferers typically die in their teens.

Until now there has been no cure and no hope of treatment, but the Lincoln-developed gene therapy is a potentially transformative treatment for the CLN5 patient community.

Over the past decade, Professor David Palmer and Doctors Nadia Mitchell and Samantha Murray have been developing their gene therapy in sheep with a naturally-occurring form of the disease. Continue reading

Research update: the first bilberry genome assembly

Unlike cultivated blueberries and cranberries, bilberry remains undomesticated with berries harvested from the wild. This makes it perfect for genomic analysis, to provide comparisons with domesticated Vaccinium species and as a resource for breeding better berries, including bilberries.

Bilberry (Vaccinium myrtillus L.), a deciduous dwarf shrub native to Europe, has provided nutrition for Northern European populations for centuries. It is one of the most economically significant wild-harvested berries in Europe prized for its flavour and health properties. Bilberries belong to the same Vaccinium genus as blueberries (Vaccinium spp.) and cranberries (V. macrocarpon).

A team of global researchers, including colleagues from Plant & Food Research, have developed the first bilberry genome assembly. It will be used as a reference to study genomic diversity in bilberries and provide information on the loci linked to adaptive traits and the phytochemical composition of the berries.

Bilberry genetic diversity has not been well understood and the phylogenetic relationship to other Vaccinium species has been relatively unknown. One key difference between blueberry and bilberry is the localisation of anthocyanins. In blueberries these are restricted to the skin but in bilberries they accumulate in the flesh. This study analysed the locus for the anthocyanin-regulating transcription factors (MYBA) and identified a complex locus controlling berry anthocyanin composition and localisation.

The bilberries sampled in the study came from above the Arctic Circle in the Sámi region of Finland. This paper will be one of the first to carry a Biocultural Notice label (BC).

The BC Notice label is a digital identifier that recognises the rights of indigenous peoples to define the use of information, collections, data and digital sequence information generated from the biodiversity and genetic resources associated with their traditional lands, waters and territories. The research was also undertaken in collaboration with Genomics Aotearoa.

The team is part of VacCap, a US-based consortium of Vaccinium researchers, and this new bilberry genome will contribute to a Vaccinium pan-genome initiative designed to improve berry fruit quality and market value.

The genome will be hosted on the major collaborator site Vaccinium.org.

Funding for the study was provided by the New Zealand Ministry of Business Innovation and Employment (MBIE) Endeavour programme ‘Filling the Void’ (C11X1704).

Journal Reference
Wu C, Deng C, Hilario E, Albert NW, Lafferty D, Grierson ERP, Plunkett BJ, Elborough C, Saei A, Günther CS, Ireland H, Yocca A, Edger PP, Jaakola L, Karppinen K, Grande A, Kylli R, Lehtola V, Allan AC, Espley RV, Chagné D.   A chromosome-scale bilberry genome.  Molecular Ecology Resources. DOI https://doi.org/10.1111/1755-0998.1346

Source:  Plant & Food Research

Epigenetic inheritance and reproductive mode in plants and animals

Research update:

Epigenetic inheritance, a source of nongenetic inheritance, occurs when epigenetic modifications are passed on through reproduction to the next generation.

Studying the sources and consequences of epigenetic inheritance is critical to understanding nongenetic inheritance, phenotype, and the adaptive potential of populations and species. This is particularly relevant in light of rapid environmental change, where epigenetic modifications are increasingly recognised as important mechanisms to respond to stress.

A recent review led by Plant & Food Research scientists, has found that footprints on top of the DNA sequence, acquired during the lifetime of an individual, are inherited across multiple generations in plants and animals. How a species reproduces: sexually or asexually, laying eggs like fish or giving birth like mammals, influences how often these changes are inherited.

Additionally, the review shows that events that occur during the lifetime of an individual – like exposure to a toxic substance, changes in nutrition or even variations in the ambient temperature or oxygen levels – can all can be recorded as footprints in most organisms and passed to the next generation. These epigenetic mechanisms can alter gene expression and allow species to respond rapidly to their environments, much faster than changes in DNA could achieve that, by modifying their phenotypes.

The study concludes that multi-generational persistence of epigenomic patterns is common in both plants and animals, but also highlights many knowledge gaps that remain to be filled. The study provides a framework to guide future research towards understanding the generational persistence and eco-evolutionary significance of epigenomics.

Journal Reference:

Anastasiadi, D., Venney, C. J., Bernatchez, L., & Wellenreuther, M. (2021). Epigenetic inheritance and reproductive mode in plants and animals. Trends in Ecology & Evolution    https://doi.org/10.1016/j.tree.2021.08.006

Source:  Plant & Food Research

Beef + Lamb New Zealand Genetics appoints livestock scientist

Livestock scientist Dr Jason Archer has been appointed to the role of Genetics Specialist – Livestock with Beef + Lamb New Zealand (B+LNZ) Genetics.

B+LNZ Genetics General Manager Dan Brier says he is thrilled that Jason is joining the team, bringing with him a wealth of knowledge and experience in animal genetics and breeding.

Jason, who has an Agricultural Science degree and a PhD in animal breeding and genetics, worked as a consultant with AbacusBio before  joining B+LNZ Genetics.  He had previously worked with AgResearch for 12 years.

While specialising in genetics, Jason has worked with broader farm systems and thinks strategically to solve problems and ensure solutions are applicable on-farm.

“Jason is very highly regarded in the sector and is well known to many farmers with a strong background in beef cattle (and deer) breeding and management. He has had over 25 years’ experience working in Australia and New Zealand, as well as with international beef breed associations in USA and Canada,” says Mr Brier.

Jason’s role at B+LNZ Genetics will involve providing direction to both sheep and beef programmes, providing a key link between the science, data strategy and practical application of genetics across the industry.

“Jason will work across NZ (including with the dairy industry) and internationally to ensure our farmers get the best bang for their buck. More importantly, Jason will ensure that the needs of our breeders and commercial farmers are met, and they have the tools they need to continue to produce some the world’s best naturally-raised red meat now and into the future.”

Dr Archer sees his role as thinking strategically to determine the industry’s future requirements and shaping what needs to be done to meet those.

“I’m very much looking forward to talking to industry and farmers, seeing the big picture and helping to shape and deliver our programmes to provide as much value to our industry as possible.”

Jason will be based out of B+LNZ Genetics’ Dunedin office.

Source: Beef + Lamb New Zealand

Bull burps may hold the answer to breeding climate-friendly cows

A Waikato trial’s discovery of a possible link between bulls’ genetics and the amount of methane they produce raises that New Zealand dairy farmers might be able to breed

The pilot trial, by artificial breeding companies LIC and CRV with funding from the New Zealand Agricultural Greenhouse Gas Research Centre, measured feed intake and methane emissions – in the form of burps – from 20 young bulls destined to father the next generation of New Zealand’s dairy cows.

LIC Chief Scientist Richard Spelman says results from the pilot trial are promising.

“Methane production primarily relates to how much an animal eats. We’ve accounted for this and we’re still seeing variation which suggests genetics plays a role in a dairy bull’s methane emissions – now we need more data to prove it.” Continue reading